As Clarenceux, Cooke was responsible for arranging the funerals of all knights resident south of the River Trent[7] In this capacity he oversaw the "magnificent" state funeral at St Paul's Cathedral of Sir Philip Sidney, who died in Flanders on 17 October 1586.[7][8] Detailed drawings of the funeral procession on 16 February 1587, with its hundreds of mourners, were published as The Procession at the Obsequies of Sir Philip Sydney, Knight, drawn and invented by Thomas Lant, Gentleman, servant to the said honourable Knight, and engraven on copper by Derick Theodore de Brijon, in the city of London. 1587.[8]

Cooke had campaigned to be appointed Garter (with the support of Dudley, by then the powerful Earl of Leicester),[9] and William Dethick, who secured the appointment, later charged Cooke with encroaching on the traditional privileges of Garter King of Arms. In 1595, after Cooke's death, William Segar, Norroy King of Arms, sided with Dethick, criticising Cooke for his inability to write clearly and for making many grants of arms to "base and unworthy persons for his private gaine onely."[3][10][11]Ralph Brooke, York Herald and sometimes deputy to Cooke, complained in 1614 that Cooke had granted more than 500 new coats of arms during his tenure.[11]

In 1530, Henry VIII had issued an instruction governing the conduct of heraldic visitations, in which Clarenceux and Norroy Kings of Arms (or their deputies) were to tour their areas of authority, recording coats of arms and pedigrees of armigers, with powers to forcibly prevent the bearing of unauthorised arms.[12]

Cooke's other writings in manuscript include An English Baronage, Heraldic Rudiments, An Ordinary of Arms and A Treatise on the Granting of Arms. On one copy of An English Baronage the antiquarianSir Simonds d'Ewes wrote a title concluding "in which are a world of errors, ergo caveat lector."[3][9]